Wednesday, December 20, 2006

Well just got an email from Chris Surridge of PLoS One saying their Beta Site is open to the public. I am excited by this new journal and system and plan to submit many of our papers there. People should check it out for themselves and hopefully give comments to them to make the system better. Some detail from the email is given below.

The first paper there that struck my eye is a paper on polyploidy in halophilic Archaea. This paper, by Sebastian Breuert, Thorsten Allers, Gabi Spohn, and Jörg Soppa suggests that polyploidy is more common in archaea than was previously appreciated.

----------------------------The email says:

Before your first visit, I want to let you know about the inherent challenges of this project and the philosophy that compels PLoS to confront them.

We want to speed up scientific progress and believe that scientific debate is as important as the investigation itself. PLoS ONE is a forum where research can be both shared and commented upon - we are launching it as a beta website so that the whole scientific community can help us develop the features.

What makes the site beta? Not the content, which features peer-reviewed research from hundreds of authors across a diverse range of scientific disciplines. It's the additional tools and functionality surrounding these papers that will be continually refined and developed in response to user feedback.

It is this union of continually evolving user tools provided by the Topaz publishing platform and extensive content that will make PLoS ONE a success.

....

The first beta release of PLoS ONE features tools that allow users to annotate articles and participate in discussion threads. Our goal is to spark lively discussion online and we'd like to invite you to participate. Future updates will include user ratings for both papers and the comments made about them, personalized content alerts and much more.

We will be watching with interest to see how our new platform and software responds to high volumes of traffic and encourage you to give your feedback on your first experience via the site itself.

Tuesday, December 19, 2006

Here is an Open Access must read. Bill Hooker blogs about pushing the Open Access envelope in the area of Open Data. That is, making sure the raw data from a scientific study is available. Although there are many efforts for this, he discussed something I have never really considered which is trying to make sure the journals do not somehow obtain rights to the raw data (e.g., by having it placed onto their site as Supplemental Information).

He has a suggested protocol for adding an addendum to the typical copyright agreement one might make with a journal, which is, in my mind, a great first step.

This site is a collection of audio and video of lectures that were for the "Microbes, Minerals, and the Environment" symposium. The collection includes talks by David Stahl, Derek Lovely, Anna Louise Reysenbach, Faroq Azam, Jonathan Zehr, and Paul Falkowski, all relating to microbes in the enviornonment. I have not watched all of them but the ones I have seen are quite good.

Well, the good news keeps pouring in for science education and the teaching of evolution. The Cobb County School Board, which had tried to insert religious points of view into the teaching of evolution, have backed down. They had placed stickers on biology textbooks that read

This textbook contains material on evolution. Evolution is a theory, not a fact, regarding the origin of living things. This material should be approached with an open mind, studied carefully and critically considered

Yet, of course they did not label any other area of science in this way. AP reports that

It is nice to see that they have had a change of heart, or at least have realized that they would lose this fight. Either way, science and education win this round. Unfortunately, the proponents of Intelligent Design, will try again and again. And they should be fought every step of the way to keep them from attacking the teaching of evolution in science classes.

All these recent stories on the Neanderthal sequencing projects reminded me of a short story I wrote while in graduate school. I wrote this story for a class taught by Carl Djerassi, a professor at Stanford and an author of a variety of what he calls "Science in Fiction" novels. In these, he writes about the workings of science and thus the name of the genre.

For this class all the students were supposed to write short stories that were then shared among the students and with Djerassi and each week we would read and discuss two of the stories. The stories written by the other students were great overall - moving and interesting and fun to read and discuss. The class digressed at the end due to Djerassi's desire for the group to write a fiction "Renga." Renga is a form of poetry where one person writes a line and then another writes the next line and together a group is supposed to come up with a poem of interest.

So we wrote a story - with each student in the class writing a paragraph and then sending it on to the next author. In the end, the story was, in my opinion, much worse than all the individual's stories. But amazingly, Djerassi convinced Nature to publish the story and thus I am a co-author on what was the first (and probably last) short story published in Nature. The worst part of it was - Nature made us reduce the lenght of the story to fit some page restrictions. That would be fine I guess if we knew this in advance. But in the end, what this did was cause us to edit the story and remove any hints of the "Renga" nature of the story. I was embarassed by the story and wanted to use a pen name so people would not know it was me. I chose Joan Eisen but for some very particular reasons I had to change my author line back to Jonathan (long story).

OK -back to the main point. I wrote a story that is about sequencing Neanderthal DNA. And though I am not sure any more what I think of the story ... here it is.

David Cohn was unaware that, while he was camping in Death Valley, every five minutes his computer would contact U. C. Berkeley's mainframe system and download any email messages David had received since the last check. David did not find out that he had left his email program open until, fumbling for his keys outside his office, he heard his computer play two randomly selected segments of Mozart's clarinet concerto, announcing that two new messages had just arrived. David had been gone for three weeks and had come in early in the morning so he could check his email in peace before other people would arrive and start asking about his trip or reading his email over his shoulder.

Symposium ThemeMicroscopic organisms-including viruses, bacteria, archaea, and single-celled eukaryotic organisms-comprise the vast majority of life on the planet, yet startling little is known about their true diversity and the multitudinous roles that they play in the ecosphere. The knowledge that we do have tends to come from either those organisms that can be cultured in the laboratory (estimated to be <1% of all species) or those that make us or other organisms that are important to us sick. The revolution of using DNA sequences to discover and describe microbial diversity has drastically altered our view of the microbial world and its players, however. Less than two decades ago, using ribosomal RNA gene sequences, Carl Woese and colleagues proposed an entirely new classification of life, that of three domains of organisms-Bacteria, Archaea, and Eukarya-in opposition to the traditional five-kingdom schema. Now, new biochemical processes, including new forms of photosynthesis and even electricity-generating bacteria are being discovered as culture-independent and broader explorations into new habitats are performed. Yet, at the same time that we begin to uncover new hidden potential benefits of microorganisms, the news is also replete with stories of so-called emergent diseases that threaten humans as well as other organisms on the planet.

This symposium will bring together a diverse group of microbiologists and conservation biologists to explore this intersection of two fields that, until now, has not been considered in depth. We hope to address the broad questions of: How much microbial diversity is there on the planet? How does this diversity affect other organisms, both positively and negatively? How should conservation practices take microbial life into account?

Audience: This symposium will bring together scientists from the traditionally disparate fields of microbiology and conservation, including biogeochemists, marine microbiologists, disease ecologists, and microbial systematists. as well as conservation practitioners, wildlife managers, policy makers, educators, students, and interested members of the general public.

SPECIAL STUDENT PRICING WILL BE OFFERED!

CALL FOR POSTERS: The symposium will include a poster session. Details for content guidelines and abstract-submission requirements are available at http://cbc.amnh.org/symposia/microbes/.

TO RECEIVE SYMPOSIUM UPDATES AS THEY BECOME AVAILABLE, email biodiversity@amnh.org.

Thursday, December 14, 2006

There can be no greater nightmare for a medical worker than to be accused of harming their patients. Even worse, if the allegations are untrue. Yet this is exactly what has happened to six health workers who have been sentenced to death for spreading HIV among Libyan children. Today we publish urgently an essay from Council on Foreign Relations Senior Fellow and Pulitzer Prize winning author Laurie Garrett, that warns of the terrible dangers not just to these workers but to health workers worldwide, and their patients in the poorest parts of the world if the executions go ahead. The essay is part of an increasing chorus of condemnation in scientific journals including Science and Nature . AAAS has a website which gives information on how anyone can add their voice to this campaign.

Sunday, December 10, 2006

I am starting a new series here ---- finding and writing about classic papers in Evolution and Genetics and Molecular Biology that are available for free in Pubmed Central. And though plenty of classic papers are not avilable, a good collection of them are.

My first selection is Luria and Delbrück's paper from 1943 on the origin of mutations. This papers is near and dear to my heart in many ways and I still remember looking it up for the first time when I was an undergraduate. I was taking a class from Jennifer Doudna on the origin of life, and we had to write a paper as part of the class. In the class we had discussed a new paper by John Cairns and colleagues that revisitid the origin of mutations question. Cairns et al. result suggested to them at least that bacteria could pick and choose the mutations they needed for increased fitness in a particular situation (suggestive of so-called Lamarckian evolution to them). I was fascinated by this work (so much so, that it became the topic of my grad. school application essays and the topic of my first two years of PhD research in Phil Hanawalt's Lab). So I chose to write a paper on the origin of mutations.

Obviously, to write such a paper I had to go to Luria and Delbrück's work since they were the first to experimentally test the question of how much mutations pre-existed selection and how much they arose after selection. I stillremember sifting through the old journals in the library at Harvard to find this and turning the pages in teh dust covered volume to read it.

Luria and Delbrück chose as their experimental system resistance to bacteriaphage and their model organism, Escherichia coli. In their paper first the describe the theoretical underpinning of their wor. In their theory they come up with a way to do an experiment to test whether mutations pre-exist selection or arise in response to it - something now generally known as a fluctuation test. Basically the idea is simple. Take a particular form of the bacteria. Innoculate multiple test tubes with a small amount and let each test tube grow up to a dense culture. Then expose bacteria from each tube to the selective pressure. If the mutations pre-exist selection then there should be big differences between the replicate test tubes in the number of mutants since in some the mutation would arise early in the growth of the culture and in some they would arise late (this is known as a jackpot distribution). If the mutations arise after selection then each tube should have somewhat similar numbers (with some variation around a mean).

And when they did the experiments the results followed very closely the jackpot model. They stated:

We consider the above results as proof that in our case the resistance to virus is due to a heritable change of the bacterial cell which occurs independently of the action of the virus. It remains to be seen whether or not this is the general rule. There is reason to suspect that the mechanism is more complex in cases where the resistant culture develops only several days after lysis of the sensitive bacteria.

And thus they showed that mutations unequivocally pre-exist selection. Now, it turns out that their experiment had a flaw - since they were using a lethal selection (phage) the system did not really allow for a long period of time for the mutations after selection to arise (when your dead it is hard to generate mutations). The Cairns experiment (and Ryan's before him) showed that some unusual results occurred if you used a non lethal selection. So one cannot really use Luria and Delbrück's experiment to disprove the possibility that mutations arise after selection. Nevertheless, their proof that mutations can exist before selection was a fundamental discovery. And their methods were used throughout bacterial genetics for years (to this day in fact). For more detail see Access Excellence page about Luria and Delbruck.

This is such a fundmentally important paper, and it is great that this paper is available, free to all, in Pubmed Central. See below:

I took my daughter to Petco the other day again. We treat it as a zoo/aquarium which works perrty well. They have lots of fish, birds, mice, and other animals and she loves it. I know, it probably does not treat the animals exceptionally well, and I do not buy animals from there. But my daughter loves fish and this is a great way for her to see some without going too far.

If you are into cycling in any way, you should check out the route for Stage 2 of the Amgen Tour of California. The race, which will likely feature a collection of some of the top pro cyclists in the world, is coming through Davis on February 20, 2007. And they even give Davis a little plug:

Continuing east past Lake Berryessa, the peloton will head through Davis, recently named the best cycling town in the U.S. by Bicycle Magazine.

It should be a good day for the town, although I hope it is not raining too heavily. I am not sure what the plans are for closing roads and/or for town activities on that day, so if anyone out there knows anything please let me know.

From the map it looks like they will take Russell through town and then sneak on up to Covell to Road 102 and then on towards Woodland. It also looks like there will be a bonus sprint in town.

Friday, December 08, 2006

The New York Times ran an obituary today for Esther Lederberg, who passed away on November 11. Dr. Lederberg was one of the giants of microbiology and her research was the precursor for multiple Nobel Prizes and laid the groundwork for much of the molecular biology revolution. Among her many amazing pieces of work:

The isolation of lambda phage, a virus that infects the bacterium E. coli. This virus has been used as a model system for studying the molecular basis of life.

She and her husband invented replica plating, a method that revolutionized bacterial genetics.

Amazingly to me, and thanks to Pubmed Central and the American Society of Microbiology, her replica plating paper is available for free online here.

All microbiologists out there should read this paper and should say thanks for the work of a true giant in the field.

Here is another somewhat hidden gem in Davis. We have a 22 month old daughter. She gets rapidly bored with new toys. My wife discovered a great way around this. Every few weeks she goes to the Davis Resource LIbrary and Toy Closet provide by the city Child Care Services. For a $10 annual fee, you can check out up to five toys and five videos/books at a time. Although sometimes it is hard to take the toys back if our daughter becomes particularly fond of them, she always ends up enkoying the trips to select new toys. From their web site:

The Toy and Resource Library is located at 600 A Street, in Davis. Library hours are Monday through Friday from 8:00 a.m. to 4:30 p.m.

So if you have kids who get a little bored with their toys and you do not want to keep buying new ones, check out the library. Most of the toys are in great shape and the books there have also been popular in our house.

Thursday, December 07, 2006

OK. I know I am not supposed to do this. But hey, are there really any rules for blogs?

I got my first major local press story since moving to Davis yesterday. The Sacramento News and Review ran a cover story on the U. C. Davis Genome Center, featuring me, Katie Pollard, and the director of the center Richard Michelmore. I of course do not recall saying any of the things that I am quoted saying but I certainly recall saying things close to what was quoted so in this case the reporter (Ralph Brave) seems to have done a fair job. I guess I would quibble a tiny bit with my portrayal in terms of the discussion of synthetic biology (I believe it is a powerful tool but that the practitioners downplay the risks).

The best part of the story - they featured my work on the glassy winged sharpshooter symbionts that we published in PLoS Biology earlier this year. That is (hopefully) good for me since the sharpshooter is a big deal out here in N. California since it is a vector for Pierce's Disease in grapes. Plus, they were able to use a figure from my paper since of course, the paper in fully Open Access. So my work gets some extra exposure that might have been more difficult for the paper to pull off if it was published in a non Open Access journal. In essence, Open Access publishing is the gift that keeps on giving. As long as I keep getting credit for it, it is great for me that people do not have to get permission or pay a fee to use figures from my papers.

Wednesday, December 06, 2006

Scientists from NASA have reported what appears evidence that not has Mars has water in the past, but that it has flowed on the Martian surface in the last seven years. When comparing photographs of the same site in 1999 and 2005 taken by the orbiting Mars Global Surveyor, the scientists found

appearance of a lightly-shaded patch that has all the hallmarks of being caused by water bubbling up from under the Martian surface and running down the 30 degree slope

While there may be other explanations, the pictures are stunning. If this is water, I think we have to start to come to grips with the high probability that life will be found on Mars. In other words, not only might life have existed there in the past, but I think it is reasonably likely that there is life there now. Now before you get all hoity toity on me - I am not talking about little green men here. But possibly little green microbes. Or little pale microbes that use chemical energy to fix carbon and grow. Such microbes are of course all over earth, in the deep sea, in hot springs, in tidal flats, in animal guts. The real questions (again, if this is really water) the become:

could life have evolved separately on Mars?

could microbial life from Earth have seeded Mars?

I think the answers to both questions, though unclear, could potentially be yes. For question 1, if we look at the origin of life on Earth, most studies now suggest it happened over a relatively short time scale (a few hundred million years) and possibly much faster. It may in fact have been somewhat inevitable - as long as the conditions for chemical evolution were present in the Early earth. This chemical evolution could have then set up the possibility for life to have evolved. Though the exact steps are unclear for the origin of life on Earth, it is not far fetched to imagine that they could have occured on Mars as well.

As for question 2 - I think life easily could have been transported between the two planets. All you really need is for a meteorite or comet collision with Earth to blast some moderately sized pieces of material off of Earth into space. Microbes in such material could have survived for some period of time on such pieces in space (remember, many microbes do not need oxygen, and can survive incredibyl harsh conditions on Earth). Imagine if a big piece of Earth was knocked off the planet - microbes in the center of such a piece would be protected from some of the radiation and other stresses of space. And you just need one of these pieces to end up on Mars for the cross-seeding event to occur. Of sure, there are a series of assumptions here and a multiplication of low probability events. But we can make up for low probability by multiplying by 3.5 or so billion years - the amount of time that life has existed on Earth.

So this raises one final issue for me. The person with the greatest job title in the world - John Rummel, better get moving. He is the "Planetary Protection Officer" for NASA - charged with protecting other planets from Earth and Earth from other planets. One of his main jobs is to think about how to make sure the Martian missions do not bring microbes with them to Mars so that if microbes are found there we can assume they are from Mars not earth. Unfortunately in my google searches about this it seems Dr. Rummel has been promoted within NASA and I cannot figure out who took over his old job. Does that alas mean we are temporarily without a planetary protection officer? I hope not.

Whether it turns out life exists or existed on Mars or not, the finding of apparently flowing water on the surface is wildly exciting and proof to me that Mars missions are critical to our understanding of the world around us.

Friday, December 01, 2006

There is a potentially controversial and very interesting article in the journal PLoS Pathogens on Flu Evolution. The study was led by Edward Holmes at Penn State, and co-authored by many researchers including colleagues of mine at my former institution TIGR. They performed a detailed evolutionary analysis of the cmplete genomes of 413 influenza A viruses of the H3N2 type (the H#N# system refers to the subtypes of Hemaglutanin and Neuraminidase genes).

The virus genomes were sequenced at TIGR using a high throughput flu viral genome sequencing protocol originally developed at described by Elodie Ghedin and colleagues here and here. The viruses they selected were from across New York State as part of a surveillance program.

Using a variety of evolutionary analyses including phylogenetic reconstructions and examination of substitution patterns, they come to a surprising conclusion - that

stochastic processes are more important in influenza virus evolution than previously thought, generating substantial genetic diversity in the short term

This may seem somewhat uninteresting to many out there but if true it is critically important in fighting flu and in understanding viral pathogen evolution. Right now there are substantial efforts to try and predict what future dominant flu strains will look like. These predictions tend to rely on assumptions that positive selection of viruses is critical in generating and maintaining diversity. If stochastic processes are as important as Holmes et al conclude, it would mean that more intensive monitoring of flu is needed in almost real time (since predicting random events tends to be, well, very hard).

I confess I have not tried to evaluate whether or not I think their conclusions are correct, but on first glance they seem sound. This just goes to show that general genomic surveys that try to be relatively unbiased in their sampling can reveal substantial novel patterns not seen before in highly target genome sequencing projects.

Monday, November 27, 2006

I had a good Thanksgiving weekend this year - spending time with family and friends. But as I go back to work this week I have now gotten somewhat depressed over something I did Sunday night. I decided to remove myself from the UC Davis internet proxy to see how many of my past papers that I have published I can obtain without the UC subscriptions. So I went to pubmed, and typed in my name (Eisen JA) and got most of my papers, which are listed at the bottom of this blog (some do not come up due to publication off the pubmed grid or due to co-authors screwing up my initials). (NOTE - LISTING DELETED 4/09 BECAUSE THE FORMATTING IS ALL MESSED UP)

And then I went to see how many of my papers were freely available and how many were not. What I was most interested in was - what is the deal with papers I wrote before becoming an Open Access convert? For many it is easy to figure out if they are freely available - Pubmed has a link saying "Free in PMC" which refers to Pubmed Central. For others, it was a little trickier.

The results were both good and bad and a summary is below. A few things struck me. First, a lot of my life's work is not readily available without paying other for it. In the day and age of the internet, this means that these papers will simply be read less and less as time goes by. And that makes me very sad. If I had chosen to publish those papers in other journals, anyone in the world could get them at any time. Thankfully I did publish many papers in journals like PNAS, and ASM journals, and NAR - journals that have now decided to release them to Pubmed Central. And also thankfully (but less so) I published some papers in journals that have at least made them freely available on their web sites.

Most surprisingly to me is that a reasonable number of my papers in Nature are freely available on the Nature web site as part of their Genomics Gateway program. Nature deserves serious kudos for doing this and they stand out compared to Elsevier journals (which do not seem to ever do this) and even Science. This is disappointing as Science is published by a scientific society but apparently does not seem to care much about access to publications. Nature, a commercial publisher, is in my opinion doing more for scientific openness than Science. Now, Nature has a long way to go, but I am SO glad I listened to their editors like Chris Gunter and Tanguy Chouard who made a big deal about the Genome papers being free. I did not think it was that big a deal, but in retrospect they were ahead of me in thinking about availability. Plus Nature clearly makes more of an effort to provide free online material than they have to - and certainly make more available than Science.

So in the end - I am sad about my partially wasted past. But I am pleasantly surprised that at least some papers I thought would be more restricted are actually free (although only on the Publishers site for now - Hopefully these journals will submit them to PMC at some point). I guess - you win some and you lose some and some are somewhere in between.

******************
Summary of openness --- other scientists should do this exercise

Saturday, November 25, 2006

I am astonished so few people I have met talk about the Vic Fazio Yolo Wildlife Area that is located between Davis and Sacramento. It is a stunning place in terms of bird life and also in terms of just being able to go for a little hike near to town.

I first tried to go there last winter, but there were sings up saying the whole place was closed due to flooding. I guess I forgot about it until last month, when I was searching for things to do with my 21 month old daughter. She really loves water and birds, so I figured I would give it a try.

So I headed out with my Burley Bike Trailer in the back of the car (if I knew how close it really was I probably would have biked there). And we went over at about 10 AM on a really foggy day. All it takes is a little drive towards Sacramento. And bam - you are there. I had no idea where to go in the preserve and ended up at a little trailer that was taking hunting registrations. But the "official" there told me where there were some nice places to walk around. And we parked and then went for an hour walk. And we saw 1000s upon 1000s of ducks and shorebirds and many hawks as well as a lot of other types. My daughter did not want to leave.

I have now gone back two other times and each time has been very nice. One of the trips there we were able to see a giant flock of what looked like snow geese off in the distance towards Sacramento, and we also saw a Sora Rail as well as many other relatively hard to find species. Given that this place is SO close to Davis, I am surprised I have not seen more people there.

Wednesday, November 22, 2006

So I saw this add on my site for NextGenCode. It was very cryptic so I went to their site.

They make their site seem like they are a Biotech company promoting genetic engineering as a tool in life enhancement. But looking at their articles and other material it became clear this was a spoof of some sort. The best part of their web site are the ads, like the one for Anhedonia and the one for Losing Blondes (about blondes going extinct in 200 years). I was guessing that this was some spoof put out by people to make fun of the synthetic biology field, but then I gave in a decided to google the company.

This is when I found the Wall Street Journal article that says they are a marketing ploy for a Michael Crighton novel. (I had not clicked on the link about a book stealing trade secrets form the company, but if you do, you get a story about Crighton's novel stealing their ideas). While some may find the slight of hand they are using here to be deceptive or malicious, I think it is pretty funny. It did not take long for me to figure out it was a spoof of some sort and it was kind of fun trying to figure it out.

Good to see that my site is being used for important advertising. Some day I will discuss the ads on my site for Intelligent Design proponents.

Of course, any blog about Crighton would be incomplete without mentioning his scientific "credibility" or the debate about it. He has clearly written some interesting science-related books over the years and in many of them the science is not completely absurd. But his anti-global warming book, State of Fear, made Crighton seem like an anti-science advocate. Personally, I never read the book so I cannot comment about the issue directly. But here are some stories about the book for people to look at.

Tuesday, November 21, 2006

In the world of scientific research, perhaps the most critical step is the acquisition of funding to do research. A key component of grant reviews these days are "Release Policies" for data, tools and research materials. In general, the more "Open" one is with these release policies, the more likely one is to get a grant. This of course makes great sense. If one is going to keep ones data or tools or material private for as long as possible, then one is not advancing science as rapidly as someone else who did the same work but also released everything rapidly.

I believe now is the time for the same thing to be done regarding Open Acces publishing. One can use the same litmus test here. Imagine two grant proposals, to do identical work. And furthermore, asssume the researchers will succeed in their work. And one researcher promised to publish in an Open Access manner while the other promises to publish in a non Open manner. Again, assuming everything else is equal, I think the proposal promising Open Access publishing HAS to be scored higher than the one promising non Open publishing.

Certainly in NSF proposals this could be considered as a component of the Broader Impact criteria and people should write it into their grants. If anyone has any ideas about how this could be specifically incorporated into NIH or DOE or other grants please let me know.

So I call on researchers who support Open Access publishing in any way to start to bring this up on grant panels and in grant reviews. And to score proposals accordingly. That is, if someone has a record of publishing in Open Access journals, they should be moved up a notch compared to others. Just how much is a "notch". That should be up to individuals. But it is the principle here that is important - publishing in Open Access journals should be a component of grant reviews.

Saturday, November 18, 2006

Reuters is reporting on a speech by Kofi Annan, Secretary General of the United Nations, in which he

warned of “catastrophic” results if recent advances in biotechnology, including gene manipulation and work with viruses, fell into the wrong hands.

He also said

“We lack an international system of safeguards to manage those risks,” he said. “Scientists may do their best to follow rules for responsible conduct of research. But efforts to harmonize these rules on a global level are outpaced by the galloping advance of science itself.”

He even suggests that the time is ripe for international governing bodies much like was done for nuclear energy in the 1950s. Is this a ploy to use the current animosity towards biotechnology in Europe to give the UN something new to do? Clearly, the US would not sign on to such things with the current administration (or probably any administration). But I certainly find it interesting that he is pushing this. I wonder if he is specifically worried about synthetic biology too or if this is just more concern for genetic engineering in general.

Thursday, November 16, 2006

So - we now have data and papers relating to some genome sequencing of DNA apparently from a Neanderthal fossil. I must say, even though I am a skeptic of much of the work on ancient DNA, I find the idea of sequencing the genome of a Neanderthal to be pretty cool. Perhaps more importantly than the scientific uses of this information, the sequencing is a brilliant public relations coup for genome sequencing. It is also a potentially useful tool in science and evolution education.

I will spare everyone my worries the scientific value of this work for now and am just using this post to collect links that I have found to be useful regarding Neandethal ancient DNA.

Wednesday, November 15, 2006

Evolution fans have to check out the pumpkins at this site. I found the site by browsing around the "ClutterMuseum" blog (I was checking it out because the author poster to my blog about Davis, CA). Now, I know the FSM (Flying Spaghetti Monster) can be considered an in your face response to the intelligent design movement. But personally, the ID movement needs to be made fun of even more and the FSM is one of the best ways to do that. For more information you can read the "About" part of this blog.

I went to Long's today on Covell to drop off and then pick up a prescription. In the time I was waiting I decided to check out their "Garden Center." I was just curious and did not have high expectations when I went in. Well, I can say without a doubt that I was underwhelmed. It was more like a plant graveyard than a Garden Center. There were multple dead trees in pots there, some of which were not even upright anymore. And many of the perennials seemed dead too. It looked like nobody had even been in there in weeks. You would think at some point they would reduce their prices to try and sell stuff before it died but apparently not - the prices were nothing special even on the nearly dead stuff.

I have been checking out the various nurseries and garden cente's in the area looking for a few things to jazz up the yard. Ace Hardware is OK but I almost never end up getting anything there despite browsing for a while. Redwood Barn on the other hand, is a dream come true. We just bought a lovely tree there - not too expensive - but that is beside the point. Most importantly, the workers there know their stuff and spent the time with me to discuss what type of tree we wanted and they came up with 4-5 suggestions. Perhpas Long's shold ditch their Garden Center or maybe just let it grow wild.

Tuesday, November 14, 2006

Well, U. C. Davis (where I work) shows that it is both hip and dedicated to Science research with a new "Research Blog" put out by its University Communications office. It is called Egghead and its goal is:

Egghead is a blog about research by, with or related to UC Davis. Comments on posts are welcome, as are tips and suggestions for posts. General feedback may be sent to Andy Fell. This blog is created and maintained by UC Davis University Communications, and mostly edited by Andy Fell.

I am not sure how many other Universities have an officially sanctioned blog from the press office, but I could not find any.

My favorite post at Egghead so far is the one about a website called Adopt a Microbe. There is
absolutely no Davis connection to this site yet the wrote a tiny blurb about it anyway. I hope they continue to do things like this - it can get tedious if the blog is all about promoting Davis research only. It will certainly get read more if there is a diversity of stuff there.

It is good to see that Biology is the top subject there ... not that there is anything wrong with other fields but one of the reasons I wanted to move to U. C. Davis was because of the amazing diversity of biology-related research going on on campus.

Now if they could only get a weekly podcast going ...

If anyone out there knows of other Universities with interesting Blogs from the press office, let me know.

Monday, November 13, 2006

The Farmer's Kitchen Cafe, which is part of the Natural FoodWorks Store, is possibly the biggest hidden gem of a restaurant in Davis. They specialize in :

delicious, homemade bioregional foods, free of gluten and casein. Your food is made with locally grown and organic fruits and vegetables, free range meats and wild fish. No aluminum pans, no hydrogenated fats, no microwaved foods, no unnatural additives.

Although the service there can be a little slow, that is part of the point. This is not a fast food restaurant. It is fresh, in season, homemade, and usually organic or at least local. Last time I went I had the chicken noodle soup, which was, I have to say, even better than mom used to make. It has a nice simple clear broth, a smattering of flavorful veggies and chicken, and a good helping of clearly top of the line noodles. I also had an organic eggplant sandwich with pesto and feta cheese that was nearly perfect. The eggplant was creamy and intermixed with the pesto into a spread with no hint of the bad eggplant flavors one can get sometime. Plus, there is a great basket of miscellaneous crayons and toys that our daughter spent much of the time playing with.

This is one of my favorite places in Davis and definitely worth a visit, especially if you are into sustainable, organic or local foods. Check it out at 624 4th Street or at their website.

Friday, November 10, 2006

A sea urchin genome has been sequenced and there are some really interesting findings that have been reported based on analysis of the genome. For example, there appears to have been a large expansion of genes involved in the innate immune system in the species sequenced, Strongylocentrotus purpuratus.

All the good science aside, what most struck me were some of the ridiculous quotes attributed to some of the researchers in this project in stories and press releases. For example, in an article on MSNBC, George Weinstock says

“The sea urchin is surprisingly similar to humans,"
"Sea urchins don't look any more like humans than fruit flies, but about 70 percent of sea urchin genes have a human counterpart whereas only about 40 percent of fruit fly genes do."

Apparently, George was glossing over the reason this organism was chosen for sequencing in the first place. If you go to the NHGRIs web site you can get the white paper written that led to the selection of this species for sequencing. Perhaps the most important reason is that evolutionarily the sea urchin is closer to humans than fruit flies are. Therefore, it should only be a surprise to someone who does not know the evolutionary position of this species.

Perhaps even more appalling is the discussion of the apparent large number of genes for light sensory systems in this species. Again, Weinstock is quoted:

“There is not a lot of light at the bottom of the ocean, so it is not clear what they might be ‘seeing,'" Weinstock said. "This is certainly an area that will be studied intensively as a result of the genome project.”

I can only view this as some sort of joke. First of all, blind cavefish still have the genes for light perception even though they do not see. This is because it takes time for such genes to disappear. Second, apparently George has never really thought about where this species of sea urchin is found. It is found in the intertidal zone -- hardly the dark depths of the ocean. I could go on and on but I will just get more annoyed. In this case, Weinstock has proven that many Genome Scientists are almost completely clueless about the organisms they are working on. Which is a shame. Becuase sea urchins are fascinating creatures and the fact that they are more closely related to humans than are most other invertebrates is one of the main reasons they have been a focus on so much research up until now. Oh well ...

She sent this to an email list for ciliate researchers. I am writing about this in my blog because a blog is where you are supposed to write things these days when you are pissed off. Why am I pissed off about this? Well, the Paramecium paper makes no mention whatsoever of our paper on the genome of a close relative of Paramecium (Tetrahymena thermohila for those interested) which was published in August. And they do not even explicitly mention the Tetrahymena genome project (even though they say they took our data and used it). I guess I am not too surprised since their paper is published in Nature, which recently seems to be taking many liberties with referencing things in Open Access journals (ours was in PLoS Biology).

What is most annoying about this whole thing is that Linda Sperling is on the Scientific Advisory Board of our project, and has been privy to all of our work from the inside and was I am sure fully aware of our paper being accepted long before theirs was. Common courtesy in science would have been for them to have made a reference to our paper in press or at least our project. But for whatever reason, they carefulyl crafter their words to make no mention of our work. Interestingly, here is the email I sent to the same ciliate list on August 29, 2006

For those interested, our paper on the Tetrahymena MAC genome has been published online at PLoS Biology

Strikingly, their paper was then accepted August 31, 2006. I hate to believe in conspiracies, but it seems just a little too coincidental that their was accepted just after ours was published. And yet still no mention of our work in their paper. Hmmm ...

Fortunately, since our paper was in PLoS Biology, they cannot say "sorry - we did not have access to it." Whatever they say, I can say clearly that Linda Sperling will not be invited to our next SAB meeting.

Monday, October 30, 2006

Anyone interested in scientific publishing and/or the flu should check out a new paper in the journal Biology Direct. The paper suggests a new way of thinking about flu evolution. Whether you agree with the authors or not (I am still not sure), what is most interesting about this to me is that the reviews are posted online as are the authors responses. See the paper here and some stories about it here and here.

Biology Direct is an Open Access journal that is experimenting with the peer review system. Their experiment is quite intriguing in its methods. For details see here and here.
Basically, the author is charged with selecting reviewers and then getting the reviews. Then the paper can be published along with the reviews, whether they were positive or negative. The author can make changes based on the reviews or can choose not to. Thus someone could publish complete crap, but since the reviewers will be named publically, hopefully the reviews will indicatethat it is crap. The key to this is that the author has to select people from the Editorial Board that then select the reviewers. So as long as the Editorial Board is reasonable, the review process should be OK (note - I am on the Editorial Board although I have not been asked to do anything yet).

Do I like this system? I am not 100% sure. But I admire Eugene Koonin and colleagues for trying something different and giving the world an example of a possible way to get around the flaws of the current review system. Of course, to me, the most important thing is that the journal is Open Access, which means that anyone out there can get a fascinating look at peer review for free.

For example, people should really check out the paper and the reviewers comments and the authors responses. Or even better check out some other papers in the journal. It makes for a good read.

Wednesday, October 25, 2006

75 science professors at Case Western Reserve University in Cleveland have signed a letter endorsing a candidate for the Ohio Board of Education.

This is great news if you ask me. Scientists seemed to be emboldened to play more of a role in politics. I think this is due to some of the recent pushes from anti-science coalitions, like the supporters of "intelligent design" as a scientific theory (which it is clearly not).

We desperately need more of this type of thing - with scientists speaking up. I do not want scientists to choose sides in truly political debates. And I hope scientists will avoid being too arrogant - such as when some suggest science can solve all the worlds woes. But when sound science is being ignored or belittled by politicians, scientists should speak up. The evolution debate is but one example. There are many more issues where sound science is being misused or ignored (e.g., global warming).

So - I recommend all scientists consider doing something to get involved. Lend your support to the folks in Ohio (e.g., Lawrence Krauss organized the group to write the letter). Or join an organization like SEFORA a new science based political action group. But just don't sit on the side and say "scientists should not get involved." If all scientists keep doing that, we are in deep trouble.

The latest buzz in genomics is about the honeybee genome. The people working on this genome have really done a good job of organizing themselves (a sort of model social genomics network in a way). They have a veritable slew of papers coming out this week on various things about the genome and about honeybees that were learned by making use of the genome.

There is an entire issue of Genome Research dedicated to studies of the honeybee (see the press release here) including papers on rates of evolution, circadian rhythms, chemical sensing, sex and death (of course), and even the royal jelly. If you don't know what royal jelly is, do a google search for that. There is also an overview article in Nature and a genome report in Science. In total 170 researchers were involved in these papers.

Mind you, I am disappointed that these were not published in Open Access journals. And this is particularly sad given that the funding came from the NHGRI, the same group of sanctimonious individuals who kept talking about how the "public" human genome project was "open" in every way for the betterment of humanity. Unfortunately, what they mean by "open" even for the human genome project is a bit of a misnomer. They meant that people could look at the data immediately. But they restricted how people could use the data, despite their attempts to pretend otherwise. Consistent with this, the groups funded by the NHGRI generally do not publish their papers in Open Access journals. Shame shame shame.

OK, enough sniping. The honeybee is so fascinating biologically in so many ways that this genome sequence deserves a bit of extra attention. First, honeybees are social creatures. They have in fact been one of the key models in studying both the evolution of social behavior but also communication among organisms.

Another aspect of their biology that is very interesting is their genetic structure. Like other hymenoptera they have what is know as a haplodiploid life cycle with males being haploid (the result of unertilized eggs) and the females being diploid. This unusual genetics is another reason that honeybees and other hymenoptera have been studied extensively by biologists for many years. In fact, a great little bit of history about this is in a book on the history of studies of altruism from Princeton University press. One of Darwin's biggest concerns in the origin of life related to the self sacrifical behavior, especially that in honeybee colonies. Apparently, honeybees were a topic of conversation among non scientists and the non reproductive worker castes were well known to the public. Darwin struggled quite a bit to come up with a good explanation that was consistent with natural selection for why some individuals would sacrifice their lives for others.

Dawrin actually cam up with a good logical explanation for this - that some individuals would sacrifice if they were related to others who would benefit. Bees and their relatives played a large part in studies that have revealed in much greater detail how altruism can evolve. They may not be as warm and fizzy as some other organisms being sequenced, but they certainly were a good pick for a genome sequencing project.

Tuesday, October 24, 2006

I listened to a very interesting Science Friday Podcast today (I listen to them on my bike rides to/from work here in Davis, CA, the most bike friendly town in which I have ever lived). This particular podcast had as one of the guests Susan F. Wood. Some people may remember that she resigned from a top job at the FDA over what she felt was politics getting in the way of good science.

Well, rather than disappear as some higher ups in the executive branch do after quitting, she has jumped into a whole new realm. She has helped start a group called Scientists and Engineers for America. Their aim is to help elect to office people

They have even created a "bill of rights" for scientists. Among the rights they include:

Federal policy shall be made using the best available science and analysis both from within the government and from the rest of society.

The federal government shall never intentionally publish false or misleading scientific information nor post such material on federal websites.

Scientists conducting research or analysis with federal funding shall be free to discuss and publish the results of unclassified research after a reasonable period of review without fear of intimidation or adverse personnel action.

Federal employees reporting what they believe to be manipulation of federal research and analysis for political or ideological reasons should be free to bring this information to the attention of the public and shall be protected from intimidation, retribution or adverse personnel action by effective enforcement of Whistle Blower laws.

No scientists should fear reprisals or intimidation because of the results of their research.

Appointments to federal scientific advisory committees shall be based on the candidate’s scientific qualifications, not political affiliation or ideology.

The federal government shall not support any science education program that includes instruction in concepts that are derived from ideology and not science.

While scientists may elect to withhold methods or studies that might be misused there shall be no federal prohibition on publication of basic research results. Decisions made about blocking the release of information about specific applied research and technologies for reasons of national security shall be the result of a transparent process. Classification decisions shall be made by trained professionals using a clear set of published criteria and there shall be a clear process for challenging decisions and a process for remedying mistakes and abuses of the classification system.

I confess to being a little worried that they may become too partisan and to be effective I think they should try to be as non partisan as possible (although there is no doubt that the current administration has violated more of the items in their bill of rights than probably any previous administration). Neverthless, this sounds like a great idea and hopefully they can help increase the use of science in decision making.

Saturday, October 21, 2006

I just got back from the new version of the old GSAC meeting. It is now called GME or Genomes, Medicine and the Environment (or, as we like to call it - stuff Craig Venter is interested in these days). The meeting is organized by the Venter Institute and this year was one of the better versions of this meeting. There were some really interesting talks in a few topic areas (I will try and post some details about these later). But to me, the most interesting part was seeing the Venter genomics education bus (part of their Genomics Discovery program) on tour. They use this bus to go around to high schools and other places to do some genomics education.

Just before coming to the meeting, the bus apparently rolled into New Orleans (see Wired news story here). Lots of people like to complain about Venter and his style, but whatever you may think of him, I think this bus is a great idea. We desperately need more people who do science making an effort to interact with and educate people about scientific research. And since this bus is outfitten with lab equipment and various genome-related toys, it can go into a neighborhood without the best science labs and help introduce students to the fun and excitement of modern science.

Note - the photo was taken by me at the GME meeting in Hilton Head, SC. In the photo are Lisa McDonald, Jennifer Colvin, and (I think) Darryl Bronson.

Thursday, October 19, 2006

Well, the folks at the Harvard Crimson have apparently changed their mind. In a new Editorial, two writers from the Crimson discuss PLoS One and open peer review. Unlike the previous Crimson editorial (see my blogs about it here and here), the two writers of this one now come out clearly in support of the PLoS One idea as well as some PLoS ideals.

For example, the liken the battle between Open Access and Closed Access publishing to the battle over democracy

Democracy has reached a new frontier, and we’re not talking about the Berlin Wall. It’s a new decade and a new millennium, and yet another wall is crumbling—this time, not between countries, but in the domain of scientific research.

Perhaps most importantly, they end the editorial with

Initiatives such as PLoS ONE will help promote free and unfettered scientific study, supplementing and revolutionizing an oligarchic academic process. It is both ignorant and regressive to reject this democratization.

Although they did not address the previous highly ignorant editorial in their own newspaper, Yifei Chen and Patrick Jean Baptiste deserve kudos for a well written, well thought out editorial on a key topic for the whole endeavor of science.

Friday, October 13, 2006

A one page paper in Science reports on what I think is one of the most exciting findings in microbial genomics in years. The reports describes the sequencing and analysis of the genome of a bacterial endosymbiont of an aphid. This bacteria, known as Carsonella, has a TINY genome - only 160 kbp in length. This is ~ 3 fold smaller than the previously known smallest genome - that of Nanoarchaeum equitans which has a genome of 490 kbp.

I think almost certainly this symbiont should be considered an organelle. It is missing many cellular functions found even in the most reduced symbionts. Thus in essence it may not be the smallest genome of a cellular organism. But who cares how we define it. If it is a new organelle - that is amazing. If it is a tiny cellular genome - that is amazing too.

One thing that strikes me as strange is the fact that the paper is only one page long. It contains so little detail on what was done and what was found in the genome that the story is woefully incomplete. This I would guess is somehow related to a rush to publish but also likely due to it being published in Science, which has severe page restrictions.

This paper has been getting ENORMOUS press coverage for valid reasons. But I agree with Craig Venter (see the New Scientist article) that this genome is not of much relevance to efforts to create a "minimal" genome. This is because the ideal minimal genome is one that can support independent life. Carsonella, is far from independent and thus represents a really wild evolutionary story, but nothing of much relevance to minimal genome studies.

OK - so I am biased here but those interested in Open Access should check out my brother's letter to the Harvard Crimson that was published today. He wrote it in response to the lame editorial the Crimson wrote about PLoS One. Some of my favorite quotes from his letter

They did not, however, respond to your repellent effort to rally the forces of elitism to derail a project whose primary aim is to rapidly bring scientific knowledge to everyone.

....

Once they see PLoS One, we are confident that consumers of scientific papers will discover what employers have long ago: If you’re looking for the imprimatur of greatness, try Nature or Harvard—but if you want the real thing, try PLoS One or Berkeley.

Of course, I disagree with the use of Berkeley in this context. Yes it is a public school. But come one - to use Berkeley as the "anti"elitist school of the world is a big stretch. So if you want the real thing, try U. C. Davis, not Berkeley.

Thursday, October 12, 2006

Two new articles published in the last issue of PLoS Biology bring forth some wildly interesting details about the lives of endosymbiotic bacteria.

One of the articles is about the role Wolbachia may play in speciation in Drosophila species. Wolbachia are a type of bacteira that are found to infect a wide diversity of invertebrate species. These bacteria are transmitted directly from mother to offspring much like mitochondria. Interestingly, many have evolved specialized means of negatively impacting male offspring. In the PLoS Biology study, the researchers were working on a type of Wolbachia known to cause cytoplasmic incompatability in which infected male offspring cannot produce offspring with uninfected females. Since these males can produce offspring with infected females, this helps contribute to the spread of the Wolbachia in the population. To make a long story short, the current paper proposes that not only can Wolbachia apparently lead to speciation through behavioral affects on the host, but that these affects can be stimulated even in species not infected by Wolbachia, if another similar species in the same area is infected. To learn more about the study read the synopsis here. I am personally interested in this story because we published the first Wolbachia genome a few years ago in PLoS Biology.

The second story to me is even more interesting. This relates to a bacterial symbiont that is found in the gut of a stinkbug species. The paper is important because the symbiont in this case does not live inside the cells of its host as do many other gut symbionts of insects. Instead, the symbiont lives in an extracellular capsule. Interestingly, the symbiont is transmitted to offspring not directly in eggs as in many other symbionts, but indirectly. The mother deposits a mass of the bacteria near the eggs and these are then consumed by the young just after hatching (the video of this is amazing).

The paper shows that these symbionts possess many of the genomic features found in other transmissable symbionts - including small genomes, high AT contents, and high rates of evolution (you can read more about this in my recent paper on symbionts of the glassy winged sharpshooter here or in my earlier blog). Many previously thought that these genomic features were related to the intracellular lifestyle of symbionts. But given that the same features are found in these extracellular symbionts, this suggests that the shared genome features are probably related to experiencing population bottlenecks in transmission from mother to offspring. See the synopsis of the paper here.

Tuesday, October 10, 2006

Well, the newspaper of Harvard has posted an editorial about what they call "Science in Print." The editorial is disappointingly a confusing mashup of ideas, facts, and flasehoods regarding PLoS One. The Crimson folks criticize online science journals under the idea that none of them are peer reviewed. They take issue in particular with PLoS One because they think it is to have no peer review at all. Fortunately, Chris Surridge, Pedro Betrao, and others have already posted messages to the comments section online about this correcting many of the mistakes in the editorial.

What is most disappointing to me about my undergraduate institution's newspaper's actions is that they seem to have written this editorial without even taking the time to read anything about the system they were criticizing. In doing some google searches I cannot even figure out where they got some of the misinformation they cite regarding PLoS One.

I completely understand people being uncomfortable with some aspects of the PLoS One system. Any change is scary to scientists and to supporters of science. But the experiment PLoS One is carrying out is not about replacing peer review entirely. It is about modifying the peer review system slightly (basically - papers will be reviewed for techincal quality only and not things like novelty) and also about adding a better evaluation system for scientific publications. I confess, I am not sure it is the perfect idea. But the world is a very very different place than it was when the current scientific publishing paradigm was established. We need to try some new ways of publishing if science is to take advantage of the internet driven, blogging, podcasting, mashup, [insert favorite technojargon here], world.